I read this about six years ago. It is a trilogy, I believe. The story starts off with a girl who is surviving on her own, trying to find her family. Later in the book, she joins a colony where she becomes a “soldier” for the colony. Later on in the series, she is sent to a Texas prison to find someone, but gets stuck in the prison. It was a very interesting view on the dystopian young adult genre.
Possibly the Strikers series by Ann Cristy.
One hundred and twelve years after the fall, the Republic of Texas is built on two foundations: total freedom and total responsibility. Every citizen is free to do what they like, when they like, but they must take responsibility for each action. With such an ideal to strive for, life should be good and for many, it is. But there are flaws in every system and some people will always fall through the cracks.
Karas Quick has fallen through almost every crack there is. Her mother is an abusive alcoholic. Her father is a long missing Striker with four strikes against him and a date with Justice should he ever be found. At sixteen, she just has to survive two more years until she reaches majority without getting five strikes. But it’s getting harder not to fight back and earn yet another strike tattoo on her neck.
Everything changes one ordinary day watching the latest catch of smugglers and Strikers being returned for justice. Within their ranks is the father Karas can’t even remember. And he has a message.
It's only Karas's father who is missing, though she has little to do with her mother. The first book was published in 2014 so it fits with you reading it about six years ago.
In the later books Karas and her friends escape back to Florida, but they are sent back to Texas on a mission to get information about a bioweapon Texas is developing.
I don't think there are any aliens in the story. You mention aliens in the title but don't say what part you remember aliens playing in the series.
Possibly the The 5th Wave series by Rick Yancey, published 2013–2016.
The trilogy follows 16-year-old Cassie and her younger brother, known as Nugget, as they try to survive after aliens have taken out most of humanity. During the course of the first book, Cassie gets separated from her younger brother, and he winds up becoming a soldier in a troop purporting to be fighting the aliens.
During the last book, Cassie and several other characters break into an alien base, and Cassie winds up undergoing a process that gives her the same knowledge as the aliens' agents. This may be what you're thinking of as getting trapped in a prison.
The epilogue of the book takes place in Texas, I don't remember exactly where the bulk of the series is set.